Tue Oct 11 08:29:06 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6600905 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 0.6600905 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2662 net assigned charge : 7.500024 assigned positive charge : 428.1346 centred at (gu) : 90.53431 92.01360 90.68049 assigned negative charge : -420.6352 centred at (gu) : 90.73791 91.92145 90.80689 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8039 nv = 96 ne = 84 npr = 57206 no. pairs analyzed = 57206 no. exposed pairs = 3337 no. arc points = 23495 no. surface atoms = 1124 nbur = 1685 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 503 mr = 4581 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3800000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2219 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9788077E-08 -9.7523207E-09 midg,1,midg; midg,igrid,midg -2.1479876E-10 5.8859019E-08 1,midg,midg; igrid,midg,midg 5.5241816E-08 -2.8577436E-08 gauss-seidel spectral radius is 0.9881197 estimated iterations to convergence 75 setup time was (sec) 0.6600000 now iterating at: 08:29:08 rms-change max change #iterations 0.1732317 25.11343 at 10iterations 1.8502312E-02 2.463552 at 20iterations 1.9869036E-03 0.3043957 at 30iterations 2.2436438E-04 3.1067848E-02 at 40iterations 3.2983971E-05 4.1465759E-03 at 50iterations finished qdiffx linear iterations at : 08:29:12 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 3.2983971E-05 4.1465759E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 08:29:12 4.669u 0.434s 0:05.84 87.1% 0+0k 0+0io 4pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.980271 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 1.980271 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2662 net assigned charge : 7.500024 assigned positive charge : 428.1346 centred at (gu) : 91.60235 96.04046 92.04094 assigned negative charge : -420.6352 centred at (gu) : 92.21346 95.76395 92.42065 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23495 grid for indexing accessible points = 1.400000 m= 32835 mr = 60591 m= 5587 mr = 24755 m= 394 mr = 3688 m= 10 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 690 time to turn everything in is 0.7100000 number of dielectric boundary points 35860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21033 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6600905 object centre at (A) : 0.6290007 22.57450 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5168232E-02 -6.2578744E-03 midg,1,midg; midg,igrid,midg 1.0749688E-02 5.2188560E-02 1,midg,midg; igrid,midg,midg 0.1014034 -3.2117169E-02 gauss-seidel spectral radius is 0.9987503 estimated iterations to convergence 224 setup time was (sec) 1.020000 now iterating at: 08:29:14 rms-change max change #iterations 4.822339 187.8402 at 10iterations 2.332860 66.20734 at 20iterations 1.126511 32.76688 at 30iterations 0.5483780 18.27792 at 40iterations 0.2663656 8.157320 at 50iterations 0.1294572 4.285557 at 60iterations 6.2459085E-02 1.727621 at 70iterations 3.0236175E-02 0.9250031 at 80iterations 1.4661524E-02 0.4457350 at 90iterations 7.1002543E-03 0.1964149 at 100iterations 3.4533462E-03 0.1079807 at 110iterations 1.6759433E-03 5.3756714E-02 at 120iterations finished qdiffx linear iterations at : 08:29:24 total time elapsed so far: 10.65000 # loops : 120 mean,max change (kT/e) : 1.6759433E-03 5.3756714E-02 energy calculations done at 10.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 08:29:24 10.836u 0.432s 0:11.57 97.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:29:24 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.970407 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -26.33700 27.59500 ymin,ymax (A): -3.757000 48.90600 zmin,zma (A): -1.158000 51.62600 x,y,z range (A): 53.93200 52.66300 52.78400 scale (grids/A): 2.970407 object centre (A): 0.6290007 22.57450 25.23400 number of atom coordinates read : 2809 total number of charged atoms : 2662 net assigned charge : 7.500024 assigned positive charge : 428.1346 centred at (gu) : 92.40345 99.06064 93.06104 assigned negative charge : -420.6352 centred at (gu) : 93.32007 98.64588 93.63087 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 198946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23495 grid for indexing accessible points = 1.400000 m= 104418 mr = 145902 m= 39867 mr = 86676 m= 10429 mr = 32600 m= 1763 mr = 8066 m= 160 mr = 1312 m= 7 mr = 100 m= 0 mr = 1 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 2327 time to turn everything in is 1.880000 number of dielectric boundary points 80933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 21293 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.980271 object centre at (A) : 0.6290007 22.57450 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7333300 -8.3372146E-02 midg,1,midg; midg,igrid,midg 0.1883927 0.5445138 1,midg,midg; igrid,midg,midg 0.9298720 -0.3387731 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 2.210000 now iterating at: 08:29:27 rms-change max change #iterations 10.96486 372.3130 at 10iterations 6.447286 129.0277 at 20iterations 3.783470 73.80223 at 30iterations 2.214406 43.09565 at 40iterations 1.296236 24.77196 at 50iterations 0.7566277 13.42824 at 60iterations 0.4416781 8.319756 at 70iterations 0.2577569 4.528751 at 80iterations 0.1501820 2.736067 at 90iterations 8.7678656E-02 1.439209 at 100iterations 5.1028568E-02 0.8859158 at 110iterations 2.9739689E-02 0.4812193 at 120iterations 1.7316192E-02 0.3056951 at 130iterations 1.0097724E-02 0.1585922 at 140iterations 5.8954819E-03 9.8567963E-02 at 150iterations 3.4483857E-03 6.3316345E-02 at 160iterations 2.0250629E-03 3.3445358E-02 at 170iterations 1.1995403E-03 2.1190643E-02 at 180iterations finished qdiffx linear iterations at : 08:29:44 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 1.1995403E-03 2.1190643E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.12000 DelPhi exited at 08:29:44 19.125u 0.499s 0:20.08 97.6% 0+0k 0+0io 0pf+0w